3.Application and evaluation of droplet digital polymerase chain reaction in detection of severe acute respiratory syndrome corona virus-2
CHEN Shuang ; WANG Ming-yue ; ZU Zhen ; TANG Yun ; YE Sheng ; LING Hua ; TAN Zhang-ping
China Tropical Medicine 2023;23(5):495-
Abstract: Objective To analyze the nucleic acid detection results of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) by droplet digital PCR (ddPCR) and compare with the detection results of real-time fluorescence quantitative RT-PCR (qRT-PCR), so as to evaluate the advantages and disadvantages of detection, and to provide data support for optimizing the nucleic acid detection scheme of SARS-CoV-2. Methods According to the SARS-CoV-2 specific primer probe published by the China Center for Disease Control and Prevention, a ddPCR detection method for SARS-CoV-2 was designed. One sample was selected for sensitivity test after gradient dilution; six respiratory virus nucleic acid positive samples including seasonal H3N2 influenza virus and SARS-CoV-2 positive samples were selected for specificity test; five SARS-CoV-2 positive samples were selected for repeatability test; in addition, 30 positive and 20 negative SARS-CoV-2 samples were selected for multiple clinical samples testing, and the results were analyzed and compared with those of qRT-PCR. Results The ddPCR method can specifically detect SARS-CoV-2, and directly obtain the original copy number of the sample target gene to achieve accurate quantification; the sensitivity test of gradient dilution positive samples showed that qRT-PCR detected target genes in part of the 10-5 dilution of samples, and no target genes were detected in 10-6 dilution, while ddPCR detected all target genes in both 10-5 and 10-6 dilution of samples. The detection limit of ddPCR was two orders of magnitude higher than that of qRT-PCR, and the sensitivity was higher than that of qRT-PCR; in the comparison of the repeatability test results of the two methods, the coefficient of variation of ddPCR was 1.266%-11.814%, lower than 1.729%-26.174% of qRT PCR, and the repeatability was higher than qRT-PCR; among 50 clinical samples, 30 positive samples of confirmed cases of Coronavirus Disease 2019 (COVID-19) were detected by both methods, SARS-CoV-2 was successfully detected by both methods, and 20 negative samples of COVID-19 were detected by both methods, and the results were negative, with a coincidence rate of 100.00% (50/50). Conclusion The ddPCR method can accurately quantify SARS-CoV-2 with strong specificity, and its sensitivity and repeatability are higher than those of qRT-PCR, but it also has certain detection limitations and is more suitable for the detection of low load samples. In the actual detection, the two methods can be reasonably combined to improve the detection accuracy.
4.Quantitative structure characteristics and fractal dimension of Chinese medicine granules measured by synchrotron radiation X-ray computed micro tomography.
Xiao-long LU ; Qin ZHENG ; Xian-zhen YIN ; Guang-qing XIAO ; Zu-hua LIAO ; Ming YANG ; Ji-wen ZHANG
Acta Pharmaceutica Sinica 2015;50(6):767-774
The shape and structure of granules are controlled by the granulation process, which is one of the main factors to determine the nature of the solid dosage forms. In this article, three kinds of granules of a traditional Chinese medicine for improving appetite and promoting digestion, namely, Jianwei Granules, were prepared using granulation technologies as pendular granulation, high speed stirring granulation, and fluidized bed granulation and the powder properties of them were investigated. Meanwhile, synchrotron radiation X-ray computed micro tomography (SR-µCT) was applied to quantitatively determine the irregular internal structures of the granules. The three-dimensional (3D) structure models were obtained by 3D reconstruction, which were more accurately to characterize the three-dimensional structures of the particles through the quantitative data. The models were also used to quantitatively compare the structural differences of granules prepared by different granulation processes with the same formula, so as to characterize how the production process plays a role in the pharmaceutical behaviors of the granules. To focus on the irregularity of the particle structure, the box counting method was used to calculate the fractal dimensions of the granules. The results showed that the fractal dimension is more sensitive to reflect the minor differences in the structure features than the conventional parameters, and capable to specifically distinct granules in structure. It is proved that the fractal dimension could quantitatively characterize the structural information of irregular granules. It is the first time suggested by our research that the fractal dimension difference (Df,c) between two fractal dimension parameters, namely, the volume matrix fractal dimension and the surface matrix fractal dimension, is a new index to characterize granules with irregular structures and evaluate the effects of production processes on the structures of granules as a new indicator for the granulating process control and optimization.
Drugs, Chinese Herbal
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analysis
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Fractals
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Medicine, Chinese Traditional
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Powders
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Quantitative Structure-Activity Relationship
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Synchrotrons
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Technology, Pharmaceutical
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Tomography, X-Ray Computed
5.Identification of a new subtype of blaADC produced by Acinetobacter baumannii isolated in children.
Rui-zhen ZHAO ; Qian CHEN ; Yue-jie ZHENG ; Zu-huang MI
Chinese Journal of Epidemiology 2007;28(10):1009-1012
OBJECTIVETo investigate the genotype of blaADC which was a kind of AmpC produced by Acinetobacter baumannii (AB), isolated through the detection of 28 similar strains among children.
METHODS28 strains of AB were collected and isolated from the Pediatrics clinic during 2006, and were identified through bacteria and susceptibility test using Vitex-32 automicroscan GNI and GNS cards. The genotype of blaADC was confirmed by polymerase chain reaction (PCR) and them sequenced.
RESULTS3 of the 28 strains of AB showed multi-drugs resistance, with a positive rate of 10.71%. blaADC was discovered in 17 of the 28 strains and the positive rate was 60.71%. All the 28 strains of AB were resistant to Cefoxitin. blaADC positive strains were all sensitive to Ampicil/Sulbactam, and only one of them was resistant to Piperacillin/Tazobactan. There were no blaADC genes discovered in the strains that were resistant to Ampicil/Sulbactam or Piperacillin/Tazobactan. There were changes of amino acids on the site 4, 242, 342 and 376 in the sequence of blaADC of No.2 strain, comparing to gi /7258342/ emb /CAB77444. 1/ in GenBank.
CONCLUSIONAbove 60% of the AB isolated in children were carrying blaADC while a strain was collected from them at random. When they were undertaken nucleotide sequence analysis, significant difference was found from the others that landed in GenBank, which identified itself as new subtype.
Acinetobacter Infections ; microbiology ; Acinetobacter baumannii ; classification ; drug effects ; genetics ; isolation & purification ; Amino Acid Sequence ; Anti-Bacterial Agents ; pharmacology ; Bacterial Typing Techniques ; Child ; DNA, Bacterial ; genetics ; Drug Resistance, Multiple, Bacterial ; genetics ; Genotype ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; beta-Lactamases ; genetics
6.Epidemiological analysis of plague in Qinghai province between 2000 and 2009
Ke-mei, WU ; Yong-hai, YANG ; Yuan-zhong, WANG ; Xue, WANG ; Zhi-zhen, QI ; Zu-yun, WANG
Chinese Journal of Endemiology 2011;30(4):437-440
Objective To analyze the endemic features of plague in Qinghai province between 2000 and 2009, discover the law of occurrence and progression, in order to provide a scientific basis for further prevention and treatment of the disease. Methods Descriptive epidemiology was employed to analyze the data from on the spot investigation, monitoring reports and papers published between 2000 and 2009. The indicators included the area, host and media distribution of animal plague and area, time, and population distribution of human plague.Results In Qinghai province between 2000 and 2009, 189 strains of Yersinia pestis were isolated from a variety of animals and insect vectors, including 77 from the marmot, accounting for 40.74%, 40 from Callopaylla dolabris,accounting for 21.16%. Positive serum antibodies against F1 plague were detected in 238 samples, including 90 samples from husbandry dogs, 63 from woodchucks. The areas with Yersinia pestis were consistent with the areas with positive serum antibodies against F1 plague, which distributed mainly along the Qinghai-Tibet railway Wulan county, Delhi and Golmud Multi-county;confirmed that there was natural foci of plague in Qinghai vole. Between 2000 and 2009, 13 events of human plague occurred, with 37 cases and 16 patients died, mortality was 43.24%.Cases were distributed in 11 townships of Tongde, Xinghai, Qilian, Wulan, Tianjun, Nangqian, Qumalai,Chengduo and Zhiduo counties. May to October was the disease season, with September the peak. Pneumonic plague disease type was the main mode of transmission of the plague and patients often contacted with airborne droplets through the air and peeling fresh Marmota. Conclusions Plague in Qinghai province is still grim,strengthening animal plague surveillance, and timely disposal of animal plague, improving the province's agricultural and pastoral areas, especially increase the disease prevention consciousness of the masses are future tasks. Work should be focused on strengthening the prevention and control of plague along Qinghai-Tibet railway,and prevent the occurrence and long-distance transmission of human plague.
7.Efficacy analysis of CAG priming regimen combined with talidomide, interferon and interleukin 2 as the induction therapy for relapsed refractory acute myeloid leukemia.
Yingling ZU ; Yanli ZHANG ; Jian ZHOU ; Huifang ZHAO ; Ruirui GUI ; Zhen LI ; Mengjuan LI ; Xudong WEI ; Yongping SONG
Chinese Journal of Hematology 2016;37(4):334-336
Aclarubicin
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therapeutic use
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Antineoplastic Combined Chemotherapy Protocols
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therapeutic use
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Cytarabine
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therapeutic use
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Granulocyte Colony-Stimulating Factor
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therapeutic use
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Humans
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Interferons
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therapeutic use
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Interleukin-2
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therapeutic use
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Leukemia, Myeloid, Acute
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drug therapy
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Recurrence
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Remission Induction
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Thalidomide
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therapeutic use
8.Characteristics and clinical outcome of T315I mutation in Philadelphia chromosome-positive acute lymphoblastic leukemia and chronic myeloid leukemia.
Juan WANG ; Yanli ZHANG ; Yingling ZU ; Zhen LI ; Mengjuan LI ; Yongping SONG
Chinese Journal of Hematology 2016;37(2):110-114
OBJECTIVETo investigate the characteristics and clinical outcome of T315I mutation in Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph(+) ALL) and chronic myeloid leukemia (CML).
METHODSThe clinical data of 118 tyrosine kinase inhibitors (TKIs) resistant Ph(+) ALL and CML cases who were detected ABL kinase domain mutation in Affiliated Tumor Hospital of Zhengzhou University from March 2014 to June 2015 were collected. Karyotypes and BCR-ABL fusion gene were analyzed respectively by R-banding, real-time quantitative polymerase chain reaction (PCR). Total RNA was extracted by TRIzol reagent and ABL kinase domain mutation was detected by direct sequencing.
RESULTSIn 23 TKIs resistant Ph(+) ALL and 95 CML cases, the rate of ABL kinase domain mutation was 60.9% (14/23) and 41.1% (39/95), respectively, and the rate of T315I mutation was respectively 34. 8% vs 5.3%, the difference was significant (χ(2)=13.586, P<0.01). The rate of mutations in chronic phase/accelerate phase /blast crisis CML patients was 38.8% (19/49), 47.1% (8/17) and 41.4% (12/29), respectively, and there was no significant difference (χ(2)=0.360, P=0.835). In Ph (+) ALL and CML patients, the median time from the beginning of TKI therapy to appearance of T315I mutation was 10 months and 19 months, the median time from the appearance of T315I to death/deadline was 2 months and 3 months, the median time of persistent hematologic response was 10 months and 16 months and the median time of overall survival (OS) was 13 months and 42 months.
CONCLUSIONT315I mutation was more easily occurred in Ph(+) ALL than CML, but two diseases are similar in the median time from the beginning of TKI therapy to appearance of T315I, the median time of persistent hematologic response and OS.
Acute Disease ; Blast Crisis ; Drug Resistance, Neoplasm ; Fusion Proteins, bcr-abl ; genetics ; Humans ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive ; drug therapy ; genetics ; Mutation ; Precursor Cell Lymphoblastic Leukemia-Lymphoma ; drug therapy ; genetics ; Protein Kinase Inhibitors ; therapeutic use
9.Study on the effect of vibsane-type diterpenoids of Viburnum odoratissimum on human HepG2 cell growth and its underlying mechanism.
Hai-Fang ZHANG ; Lin WANG ; Jie LIU ; Wen-Bin ZHOU ; Liu-Zhen ZHANG ; Ya-Jun SHAN ; Zu-Yin YU ; Ping LIU ; Hong-Wei TANG ; Yu-Wen CONG
Chinese Journal of Applied Physiology 2014;30(4):343-347
OBJECTIVETo study the antiproliferation effect on HepG2 cells and its underlying mechanism of the active chemical composition of the Viburnum Odoratissimum.
METHODS3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) reduction assay and trypan blue dye exclusion assay were used to assess the effect of vibsane-type diterpenoids on the proliferation of various tumor cells. Alterations in cell cycle and apoptosis were determined by flowcytometry. The enzymatic activity of caspase-3/7 was measured by Apo-ONE homogeneous Caspase-3/7 Assay kit.
RESULTSCompound 1 #, a vibsane-type diterpenoid, was found to significantly inhibit the growth of HepG2 cells by anticancer proliferation activity screening. It was demonstrated that the modified groups on side chain coupled to C11 site affected the cell growth-inhibition activity of compounds by structure-activity analysis. In addition, HepG2 cell line was most sensitive to compound 1 #, which induced growth arrest of HepG2 cells in a dose- and time-dependent manner. Study on the mechanisms underlying these effects indicated that compound 1 # induced significant G0/G1 phase arrest of HepG2 cells in a time- and concentration-dependent manner. Meanwhile, It was found that higher concentrations of compound (5-10 micromol/L) caused evident increase in the unmber of apoptotic cells and dose-dependent activation of caspase-3/7.
CONCLUSIONVibsane-type diterpenoids could significantly inhibit the growth of HCC HepG2 cells. Induction of cell cycle arrest and apoptosis may play important roles in their anticancer effects.
Apoptosis ; drug effects ; Cell Cycle Checkpoints ; drug effects ; Cell Proliferation ; drug effects ; Diterpenes ; pharmacology ; Hep G2 Cells ; Humans ; Viburnum ; chemistry
10.UPLC/Q-TOF MS and NMR plant metabolomics approach in studying the effect of growth year on the quality of Polygala tenuifolia.
Ying XUE ; Xiao-wei LI ; Zhen-yu LI ; Zu-ping ZENG ; Fu-sheng ZHANG ; Ai-ping LI ; Xue-mei QIN ; Bing PENG
Acta Pharmaceutica Sinica 2015;50(3):340-347
Growth year is one of the important factors for the quality of Polygala tenufolia. In this study, primary metabolites and secondary metabolites were compared in 1, 2 and 3 years old P. tenufolia cultivated in Shaanxi Heyang. The samples were subjected to ultra-high performance liquid chromatography (UPLC)-quadrupole time-of-flight mass spectrometry (Q-TOF MS) and nuclear magnetic resonance (NMR) analysis, and the obtained data were analyzed using principal component analysis (PCA) and other statistical analysis methods. In addition, content and correlation of different metabolites were also calculated. The results showed no significance between main component contents in 2 year-old and 3 year-old P. Tenufolia, but 1 year-old was statistically different. The contents of primary metabolites, such as fructose, sucrose, and choline increased as time goes on, while glycine and raffinose decreased. The contents of secondary metabolites, such as onjisaponin Fg, polygalasaponin XXVIII, polygalasaponin XXXII increased, while polygalaxanthone III and parts of oligosaccharide multi-ester including tenuifoliose A, tenuifoliose C, tenuifoliose C2 and tenuifoliose H decreased with the extension of the growth years. Growth years has important impact on the quality of P. tenuifolia and the existing growing years of commodity P. tenuifolia have its scientific evidence. This study supplied a new method for the quality evaluation of Chinese medicinal materials.
Chromatography, High Pressure Liquid
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Drugs, Chinese Herbal
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Magnetic Resonance Spectroscopy
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Mass Spectrometry
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Metabolomics
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Oligosaccharides
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Plants, Medicinal
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chemistry
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Polygala
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chemistry
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Quality Control